Yeast Protein Nhp6A Binds to Short GC-Rich Genes

Nhp6A is a small nonhistone chromosomal yeast protein that binds DNA nonspecifically. This protein is present at many promoters and transcribed regions of the genome and is involved in regulation of transcription. Recently, Nhp6A was shown to participate in destabilization of the nucleosome structure. This may explain its location at regulatory sites. However, its function in the coding regions remains unknown. In this study, in order to identify the mechanisms of Nhp6A action, we examined genomic associations of the Nhp6A protein along the entire length of the target genes, including the open reading frame. We found that Nhp6A predominantly binds to the coding regions of short GC-rich yeast genes. The observed interaction is not associated with the high GC content in these DNA loci. Thus, we can propose a specific regulatory mechanism involving Nhp6A for this group. Since a large number of the studied genes retain features of the ancestral bacterial genome, we suggest that this group can be defined as “ancient.” Presumably, this genomic distribution of Nhp6 is related to the mechanisms of regulation of gene transcription that appeared early in the course of evolution.